Contacts of the strand formed by residues 283 - 293 (chain A) in PDB entry 1HXD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A LEU 3.4 1.4 - - - +
279A ILE* 2.8 34.7 - - - +
280A ILE* 3.0 23.0 + - + +
282A ASP* 1.3 81.8 + - - +
284A GLU* 1.4 60.8 - - - +
285A ILE* 3.8 23.9 - - + +
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A LYS* 2.5 49.7 + - + +
278A LEU 3.4 2.2 - - - -
279A ILE* 3.6 19.1 - - + +
282A ASP 3.5 18.3 + - - +
283A LYS* 1.4 72.5 - - - +
285A ILE* 1.3 65.2 - - - +
286A PHE* 3.9 5.4 + - + +
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Residues in contact with ILE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A VAL* 4.1 1.0 - - - +
277A LYS* 3.4 6.1 - - - +
278A LEU* 2.5 79.8 + - + +
279A ILE* 4.5 0.9 - - - +
280A ILE* 4.9 4.5 - - + +
283A LYS* 3.8 28.3 - - - +
284A GLU* 1.3 74.5 - - - +
286A PHE* 1.3 66.6 + - - +
300A LEU* 3.9 10.3 - - + +
302A GLN* 4.9 4.0 - - + -
309A TRP* 3.0 43.3 - - + -
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Residues in contact with PHE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A VAL 3.0 21.1 - - - -
277A LYS* 3.0 46.4 - - + -
284A GLU* 3.9 6.5 + - + +
285A ILE* 1.3 78.3 - - - +
287A GLY* 1.3 57.6 - - - +
300A LEU* 4.0 9.6 - - - +
302A GLN* 4.1 13.0 - - - +
317A ARG* 3.0 58.1 - - + +
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Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A PRO* 3.2 8.7 - - - +
276A VAL 3.0 31.9 + - - -
285A ILE 4.3 0.2 + - - -
286A PHE* 1.3 78.8 - - - +
288A ILE* 1.4 63.4 + - - +
300A LEU* 4.2 9.2 - - - +
301A GLU 3.8 9.4 - - - -
302A GLN* 5.2 1.8 - - - -
317A ARG* 5.3 4.4 - - - +
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ASN 3.7 1.6 - - - +
274A ARG 3.3 28.9 - - - +
275A PRO* 4.8 6.3 - - + -
287A GLY* 1.4 74.5 - - - +
289A SER* 1.3 66.4 + - - +
290A ARG* 3.4 44.8 + - - +
300A LEU* 3.5 9.0 - - - +
301A GLU* 2.7 53.0 + - + +
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Residues in contact with SER 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ASP* 4.8 3.6 + - - -
271A PHE* 3.2 28.7 - - - +
272A ILE* 3.8 5.5 - - - -
273A ASN* 2.6 26.3 + - - -
274A ARG 3.0 5.1 + - - -
276A VAL* 4.8 7.3 - - - +
288A ILE* 1.3 72.4 - - - +
290A ARG* 1.3 73.8 + - - +
291A GLY* 3.4 8.0 + - - -
298A LEU* 3.3 25.6 - - - +
299A LEU 3.6 4.0 - - - -
300A LEU* 4.4 4.1 - - - +
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A ILE* 4.0 9.2 - - - +
273A ASN* 2.3 58.0 + - - +
288A ILE* 3.4 41.5 - - - +
289A SER* 1.3 83.3 - - - +
291A GLY* 1.3 57.7 + - - +
292A ILE 4.1 2.1 + - - +
299A LEU* 3.3 29.2 + - + +
301A GLU* 3.9 34.0 + - + +
306A ILE* 4.5 11.7 - - + -
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Residues in contact with GLY 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A TRP* 4.7 1.6 - - - -
269A ASP* 4.3 7.9 - - - -
272A ILE* 3.4 22.8 - - - +
289A SER* 3.4 8.6 + - - -
290A ARG* 1.3 79.6 - - - +
292A ILE* 1.3 65.7 + - - +
298A LEU* 2.9 14.0 - - - +
299A LEU* 2.8 23.9 + - - -
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Residues in contact with ILE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A LEU* 4.1 18.2 - - + -
173A TRP* 2.9 44.9 - - + +
258A LEU* 4.2 9.4 - - + -
262A LEU* 4.5 19.5 - - + +
265A TRP* 3.6 36.7 - - + +
290A ARG 4.8 1.6 - - - +
291A GLY* 1.3 80.5 - - - +
293A ASP* 1.3 77.8 + - - +
296A GLY 4.2 1.8 - - - -
297A ALA 2.8 9.9 - - - +
299A LEU* 4.0 8.8 - - - +
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Residues in contact with ASP 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A LEU* 4.3 0.3 - - - +
262A LEU* 4.8 2.2 - - - -
292A ILE* 1.3 83.3 - - - +
294A LYS* 1.3 57.2 + - + +
295A GLN* 2.6 45.7 + - - +
296A GLY* 2.7 15.4 + - - -
297A ALA* 2.5 50.8 + - - +
299A LEU* 3.7 24.0 - - + -
308A PRO* 4.4 10.8 - - + +
310A MET* 5.2 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il